CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		MCFold
MCC	0.564	>	0.370
Average MCC ± 95% Confidence Intervals	0.545 ± 0.174	>	0.377 ± 0.120
Sensitivity	0.541	>	0.421
Positive Predictive Value	0.598	>	0.338
Total TP	171	>	133
Total TN	27995	>	27888
Total FP	163	<	322
Total FP CONTRA	47	<	62
Total FP INCONS	68	<	198
Total FP COMP	48	<	62
Total FN	145	<	183
P-value	2.66715895098e-08

Comparison of performance of ContextFold and MCFold. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for ContextFold and MCFold).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for ContextFold and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and MCFold. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for ContextFold and MCFold).

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.545 ± 0.174
Sensitivity	0.541
Positive Predictive Value	0.598
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.58	0.56	0.63	10	512	6	0	6	0	8
2M58_A	-	-0.02	0.00	0.00	0	530	14	3	11	0	12
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.79	0.79	0.79	15	949	4	3	1	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.42	0.31	8	4735	32	9	9	14	11
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4ATO_G	-	-0.02	0.00	0.00	0	218	2	1	1	0	7
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.42	0.39	0.46	11	1824	13	6	7	0	17
4JF2_A	preQ1-II links to Rfam database...	0.57	0.50	0.67	12	1064	6	2	4	0	12
4JRC_A	-	0.91	0.82	1.00	14	608	0	0	0	0	3

Total Scores
MCC	0.370
Average MCC ± 95% Confidence Intervals	0.377 ± 0.120
Sensitivity	0.421
Positive Predictive Value	0.338
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
2M58_A	-	0.22	0.25	0.23	3	531	13	1	9	3	9
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3J20_0	tRNA links to Rfam database...	0.66	0.71	0.63	15	1195	11	3	6	2	6
3J3D_C	tRNA links to Rfam database...	0.54	0.63	0.48	12	943	13	4	9	0	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.12	3	2716	36	11	12	13	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.21	0.10	4	4720	51	17	20	14	15
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.27	10	5337	28	6	21	1	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4ATO_G	-	0.36	0.43	0.33	3	211	8	0	6	2	4
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.35	0.38	0.35	9	1176	17	3	14	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.09	0.11	0.10	3	1818	28	2	25	1	25
4JF2_A	preQ1-II links to Rfam database...	0.74	0.75	0.75	18	1058	7	1	5	1	6
4JRC_A	-	0.24	0.29	0.23	5	600	17	0	17	0	12

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.